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  <section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Link to this heading">¶</a></h1>
<section id="timsconvert-gui">
<h2>TIMSCONVERT GUI<a class="headerlink" href="#timsconvert-gui" title="Link to this heading">¶</a></h2>
<p>The GUI version of TIMSCONVERT can be run by downloading it from
<a class="reference external" href="https://github.com/gtluu/timsconvert/releases">the Github releases page for this repo</a>. Unzip the file and run
<code class="docutils literal notranslate"><span class="pre">TIMSCONVERT.exe</span></code>. See the <a class="reference internal" href="local.html"><span class="doc">Local Usage</span></a> page for basic usage of TIMSCONVERT.</p>
</section>
<section id="manual-installation">
<h2>Manual Installation<a class="headerlink" href="#manual-installation" title="Link to this heading">¶</a></h2>
<p>If you prefer to run TIMSCONVERT locally via the command line interface, you can set up a <code class="docutils literal notranslate"><span class="pre">conda</span></code> environment to do
so. Please note that TIMSCONVERT should be run under Windows or Linux. macOS is not supported.</p>
</section>
<section id="manual-installation-on-windows">
<h2>Manual Installation on Windows<a class="headerlink" href="#manual-installation-on-windows" title="Link to this heading">¶</a></h2>
<ol class="arabic">
<li><p>Download and install <a class="reference external" href="https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Windows-x86_64.exe">Anaconda for Windows</a> if not already installed. Anaconda3-2024.06-1 for Windows is used as an example here. Follow the prompts to complete installation.</p></li>
<li><p>Download and install <a class="reference external" href="https://github.com/git-for-windows/git/releases/download/v2.42.0.windows.2/Git-2.42.0.2-64-bit.exe">Git for Windows</a> if not already installed.</p></li>
<li><p>Run <code class="docutils literal notranslate"><span class="pre">Anaconda</span> <span class="pre">Prompt</span></code>.</p></li>
<li><p>Create a conda instance.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.11</span>
</pre></div>
</div>
</li>
<li><p>Activate conda environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>Install TIMSCONVERT.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">gtluu</span><span class="o">/</span><span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>TIMSCONVERT is now ready to use. See the <a class="reference internal" href="local.html"><span class="doc">Local Usage</span></a> page for basic usage of TIMSCONVERT.</p></li>
</ol>
</section>
<section id="manual-installation-on-linux">
<h2>Manual Installation on Linux<a class="headerlink" href="#manual-installation-on-linux" title="Link to this heading">¶</a></h2>
<p>Please note that while these instructions should apply to most Linux distros, TIMSCONVERT is tested on Ubuntu 22.04.3
LTS. We recommend using this distro if you encounter compatibility issues in others.</p>
<ol class="arabic">
<li><p>If not already installed, download and install <a class="reference external" href="https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Linux-x86_64.sh">Anaconda for Linux</a>. Anaconda3-2024.06-1 for Linux is used as an example here.</p>
<ul class="simple">
<li><p>Alternatively, the script can be downloaded in the <code class="docutils literal notranslate"><span class="pre">Terminal</span></code> using the following command.</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">wget</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">repo</span><span class="o">.</span><span class="n">anaconda</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">Anaconda3</span><span class="o">-</span><span class="mf">2024.06</span><span class="o">-</span><span class="mi">1</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
</li>
<li><p>If not already installed, install <code class="docutils literal notranslate"><span class="pre">git</span></code>. On Ubuntu 22.04.3 LTS, this can be done using the following command.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">git</span>
</pre></div>
</div>
</li>
</ol>
<ol class="arabic" start="2">
<li><p>Install Anaconda for Linux via the bash script that was downloaded. After installation, restart the terminal (or open a new terminal window).</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">bash</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span><span class="p">]</span><span class="o">/</span><span class="n">Anaconda3</span><span class="o">-</span><span class="mf">2023.07</span><span class="o">-</span><span class="mi">2</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
</li>
<li><p>In the terminal, create a conda virtual environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.11</span>
</pre></div>
</div>
</li>
<li><p>Activate conda environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>Install TIMSCONVERT.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">gtluu</span><span class="o">/</span><span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>TIMSCONVERT is now ready to use. See the <a class="reference internal" href="local.html"><span class="doc">Local Usage</span></a> page for basic usage of TIMSCONVERT.</p></li>
</ol>
</section>
</section>


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<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
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